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Food-dependent growth and size-dependent interactions form cornerstones in the dynamics of fish populations. Using two freshwater examples, we illustrate the importance of considering both these cornerstones for understanding system dynamics. Moreover, a proper understanding of the dynamics requires mechanistic linkages between individual-, population-, and community-level processes based on mass conservation principles. In one example, we further find that quantitative predictions of individual-level energy flows are essential for understanding the community dynamics. This mechanistic approach to understanding system dynamics is generally not reflected in fisheries models as an overview shows that only half of them incorporate food-dependent growth, and none fully observe the principles of mass conservation. As a marine example we examine patterns in the Baltic Sea system and show that no relationship between cod growth and sprat biomass is present related to the low size resolution in prey fish. Linking individual cod performance to its resource base is complicated by the many prey types cod uses over its life cycle. We conclude that an ecological perspective including size-and food-dependent processes is vital for ecosystem-based fisheries management making necessary a proper description of the interactive trophic structure as a result of mechanistic linkages between individual, population, and community processes.